Tested out some water clusters during lunch.
- MMFF94 has point charges and hydrogen bonds
- UFF does not (so water molecules push apart)

At some point I'll add some simple dynamics…

#compchem #compchemsky

Yeah, I need to do a "open URL to get the oAuth token" piece first. That's a useful example for a range of services.

And yes, the idea would be to allow users to call directly from the GUI (e.g., get back Chemeleon unit cells)

Hey #Pittsburgh - come join everyone here in Schenley Plaza to #StandUpForScience

Hey #Pittsburgh folks - consider seeing __Trouble in Mind__ at the Pittsburgh Public Theater - now until Feb. 23rd.

We went last night -- happened to also be #DivineNine night!

Fantastic production.

ppt.org/production/9...

I was laughing and my grad students suggested asking ChatGPT for a premise.

That's what's great about the @avogadro.cc plugin - it will install xtb / crest for users if it's not installed.

In a few weeks, I'll have code for submitting batches of molecules / conformers for ORCA, Gaussian, etc. or running them at once (e.g., GPU) via AIMNET from @olexandr.bsky.social

After the recent ground-breaking AI-generated textbook, I wanted to try making #chemsky cover art too 🤔

Enjoy (lol)

Cover art for a college textbook entitled "Physical Chemistry: Quantum Mechanics and Thermodynamics" featuring images of molecules, the Schrödinger equation, free energy and entropy

Why has no one posted the Rocinante from The Expanse?

Not sure these quick photos (phone wires and all) do justice to today's sunset here in #Pittsburgh

It was a nice end to an afternoon run though. 😉

I know it's not the point, but that image looks like it has 2 bonds to a hydrogen...

Welcome to all the newcomers to #ChemSky 🧪

I don't post much, but you'll get a dose of #compchem and materials discovery, a bit of #machinelearning (with skepticism) and some sprinkling of #Pittsburgh (including @pitt.bsky.social and @pittchem.bsky.social)

Enjoy some recent @avogadro.cc renders

Thrilled to post the latest work by Omri Abarbanel - a *major* step forward for micro-pKa prediction models: QupKake has prediction errors ~0.5-0.7 by combining ML and QM 🧪 #compchem

Omri beat commercial teams .. hire him 😉

We'll be sharing the model and all raw data soon.

doi.org/10.26434/che...

As someone who went to grad school as an inorganic chemist, it gives me some pleasure to finally have a free tool to click-click-click assemble iron bipyridine complexes or Ziegler-Natta catalyst models in @avogadro.cc in about the same time it takes to build an organic compound. #chemsky 🧪

Yes, although I think their table of "paper sources" illustrates that clearly. They have 3m articles from PubMed Central and 2m articles from arXiv. A lot of the rest is mostly abstracts.

So the open question is "if LLM can read more papers does it stop hallucinating?"

Hi #chemsky - I could use some help

I added a tool in @avogadro.cc to build metal complexes, including preview images of the ligands.

The auto-generated ligand images for multidentate ligands look horrible.

Anyone have ChemDraw of cyclam & triphos?

discuss.avogadro.cc/t/help-neede...

Lots of changes, including:
- Real time shading and ambient occlusion
- New tool for inorganic complexes and "add a phenyl here"
- Support for 3Dconnexion "space mouse"
- Integrated support for Orca output
- New forcefield framework

Okay, I admit. I'm now taking "molecular modeling" very literally.

Really happy with the new multi-color 3D printer I got for the lab. Looking forward to using physical models the next time I teach symmetry.